Back to Workflows build report for BioC 3.18

This page was generated on 2024-03-01 14:00:10 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 3/30HostnameOS / ArchINSTALLBUILD
BiocMetaWorkflow 1.24.0  (landing page)
Mike Smith
Snapshot Date: 2024-03-01 10:45:01 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/BiocMetaWorkflow
git_branch: RELEASE_3_18
git_last_commit: e955a08
git_last_commit_date: 2023-10-24 08:47:20 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for BiocMetaWorkflow on lconway


To the developers/maintainers of the BiocMetaWorkflow package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: BiocMetaWorkflow
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocMetaWorkflow
StartedAt: 2024-03-01 11:02:31 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 11:02:36 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 4.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocMetaWorkflow
###
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* checking for file ‘BiocMetaWorkflow/DESCRIPTION’ ... OK
* preparing ‘BiocMetaWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Authoring_BioC_Workflows.Rmd’ using rmarkdown

Quitting from lines 73-76 [createBiocWorkflow] (Authoring_BioC_Workflows.Rmd)
Error: processing vignette 'Authoring_BioC_Workflows.Rmd' failed with diagnostics:
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/git2r/libs/git2r.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/git2r/libs/git2r.so, 0x0006): Library not loaded: '/usr/local/opt/libgit2/lib/libgit2.1.4.dylib'
  Referenced from: '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/git2r/libs/git2r.so'
  Reason: tried: '/usr/local/opt/libgit2/lib/libgit2.1.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libgit2.1.4.dylib' (no such file), '/usr/local/jdk-18.jdk/Contents/Home/lib/server/libgit2.1.4.dylib' (no such file), '/usr/local/Cellar/libgit2/1.7.1/lib/libgit2.1.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libgit2.1.4.dylib' (no such file), '/usr/local/jdk-18.jdk/Contents/Home/lib/server/libgit2.1.4.dylib' (no such file)
--- failed re-building ‘Authoring_BioC_Workflows.Rmd’

SUMMARY: processing the following file failed:
  ‘Authoring_BioC_Workflows.Rmd’

Error: Vignette re-building failed.
Execution halted